666.11 - E-M for Haplotyping Revisited Biostatistics 666...

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E-M for Haplotyping Revisited Biostatistics 666 Lecture 11
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Example z We’ll estimate haplotype frequencies for the example below … BB Bb bb AA 25 30 9 Aa 20 12 0 aa 4 0 0
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Stratification vs Disequilibrium Population A Population B Ancestor Present-day
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Stratification z Due to non-random mating Eg. Mating based on proximity or culture z Allele frequencies drift apart in each group Eg. Allele frequency differences at many genes between African-Americans and Caucasians z Disease prevalences may also differ Eg. Glaucoma has prevalence of ~2% in elderly Caucasians, but ~8% in African-Americans
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For example… z Allele frequency p = 0.2 p’= 0.4 z Background prevalence k = 0.01 k’ = 0.02 z Relative Risk r = r’ = 1 z Penetrances f 11 = f 12 = f 22 =k f’ 11 = f’ 12 = f’ 22 =k’
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Implies… 64 32 4 Unaffecteds 64 32 4 Affecteds 2/2 1/2 1/1 Population 1 Sample… 36 48 16 Unaffecteds 36 48 16 Affecteds 2/2 1/2 1/1 Population 2 Sample… Sample from Mixed Population (50/50) 50.1 40.0 10.0 Unaffecteds 45.3 42.7 12.0 Affecteds 2/2 1/2 1/1
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This note was uploaded on 12/26/2011 for the course BIO 666 taught by Professor Staff during the Fall '06 term at University of Michigan.

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666.11 - E-M for Haplotyping Revisited Biostatistics 666...

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